Ok, I'm going to distill it down to their two most 'badass' moments in the movies, and both of them take place in bars. The 'Get out of my bar freak' scene, and the scene in Argentina.
This is also fair on Jackman's Wolverine to judge by the first movie only, as FB's Magneto has so far only appeared in one movie.

Both of those scenes were my favourites in both movies.
I have watched the Wolverine one countless times, and the Magneto one once, so aye, it is of course difficult to gauge how much the Magneto scene would stand up over time.

But, really, the most badass moment I feel is that moment when Wolverine sheathes his claws, gathers himself, and walks away. Rogue's reaction to that moment is just perfect, there is a momentous energy in that moment that is shared by the in movie audience.
The Magneto music in that scene is frickin great, but that little eerie piece of Micheal Kamen music that plays when Logan walks away is also perfect accompaniment, in a much more subtle way.
It is a perfect superhero moment, just 100% frickin perfect, perfect, perfect, perfect. I will never get tired of watching that scene.

Well said but still, I agree with Alexei Belyakov that Logan defending the mansion in X2 and ending with the claw pop "just shot me" scene is extremely badass and beats the bar scene in X1. I even love the Creed rematch in Origins where he learns his lesson and stabs Victor in the throat. Logan is getting the short end of the badass stick around here even though I agree 100% that Fassbender is amazing and I'll never get tired of watching that bar scene in First Class.